Explore Workflows

View already parsed workflows here or click here to add your own

Graph	Name	Retrieved From	View
	preprocess fasta Remove reads from fasta files based on sequence stats. Return fasta files with reads passed and reads removed.	https://github.com/MG-RAST/pipeline.git Path: CWL/Workflows/preprocess-fasta.workflow.cwl Branch/Commit ID: 49e29dfc5b1f7a7630831a1052f9136caa29dbf7
	count-lines5-wf.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/count-lines5-wf.cwl Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
	gcaccess_from_list	https://github.com/ncbi/pgap.git Path: task_types/tt_gcaccess_from_list.cwl Branch/Commit ID: 550682d2fe3348161eab1b8612e48a59af4ac6a5
	Per-chromosome pindel	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pindel_cat.cwl Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94
	mutect panel-of-normals workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/panel_of_normals.cwl Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
	exome alignment with qc, no bqsr, no verify_bam_id	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/alignment_exome_nonhuman.cwl Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6
	fillout_index_prefilter.cwl	https://github.com/mskcc/pluto-cwl.git Path: cwl/fillout_index_prefilter.cwl Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153
	bam-bedgraph-bigwig.cwl Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.	https://github.com/Barski-lab/workflows.git Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: bc75349ad3a7bdce82b4cd8584501f4d0280bb8d
	RNA-Seq alignment and transcript/gene abundance workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/rnaseq.cwl Branch/Commit ID: 8cee1920920ed73384fb3ab74272da9c92a20cf2
	wf-loadContents3.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/wf-loadContents3.cwl Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2